title: Identification of exosomal mRNA, lncRNA and circRNA signatures in an osteoarthritis synovial fluid-exosomal study

city: Shenzhen

first: Xiaomin

state: Guangdong

address: Baocheng Longjing 2nd Road No.118, Bao’an District

department: Department of Orthopaedics and Traumatology

institute: People’s Hospital of Shenzhen Baoan District

summary: Aims  Osteoarthritis (OA) is a common degenerative disease that is pathologically characterized by destruction of the joint matrix and reduction of articular chondrocytes, resulting in joint deformity and motor dysfunction. However, the molecular mechanisms governing this pathology have not been fully elucidated to date.  Methods  In this study, we determined the expression levels of lncRNAs, circRNAs, and mRNAs extracted from synovial exosomes of OA and control patients. A network of circRNA/lncRNA–miRNA–mRNA interactions was established using MiRanda and TargetScan software to explore OA pathogenesis. The exosomal lncRNA, circRNA and mRNA expression profiles of the OA and control groups were analysed using LC human competing endogenous RNA (ceRNA) microarrays. The differentially expressed genes were identified to determine their potential roles in the pathogenesis of OA by bioinformatic analysis.  Results  Compared with the control group, 11 mRNAs, 52 lncRNAs, and 30 circRNAs were upregulated, while 41 mRNAs, 144 lncRNAs, and 68 circRNAs were downregulated in osteoarthritis synovial exosomes. The final ceRNA network of lncRNAs and circRNAs exhibited a complex interaction between ncRNA and mRNA related to OA pathological mechanisms. An intersection analysis of the ceRNA network showed that 22 miRNAs, 45 lncRNAs, and 34 circRNAs in the PI3K/Akt and autophagy pathways correlated with 7 enriched mRNAs and may play important roles in OA pathological mechanisms.  Conclusion  Our work analysed mRNA/lncRNA/circRNA expression and displayed the ceRNA network of lncRNAs and circRNAs to profile the pathogenesis of OA in synovial exosomes. The results of this study may help to elucidate the pathogenesis of OA and may provide important references for further research attempting to identify more effective targets for the diagnosis and therapy of OA.

overall_design: male/female

first: Zhoufeng

last: Lin

first: Bin

last: Bian

first: Yuxin

last: Sun

first: Yu

last: Pan

first: Zhongjie

last: Li

first: Yong

last: Dai

first: Tun

last: Lui

first: Tengfei

last: Zhuang

first: Xiaohua


title: How experimental competition changes ovarian gene activity in free living birds: implications for steroidogenesis, maternal effects, and beyond

status: Public on Oct 03 2021

city: Bloomington

first: Kimberly

middle: A

last: Rosvall

state: IN

address: Dept of Biology, Indiana Univ., 1001 E. 3rd St, Jordan Hall

country: USA

institute: Indiana University

type: Expression profiling by high throughput sequencing

summary: The ovary plays an important role in mediating both a female’s response to her own social environment and communicating it to her developing offspring. However, we know little about the underlying genomic mechanisms that facilitate social responsiveness in the ovary. This issue is further complicated by mixed support linking female competition to ovarian production of testosterone, the often-evoked mechanism mediating both social aggression and maternal effects. Here, we experimentally generated social competition among wild, cavity-nesting female birds (tree swallows, Tachycineta bicolor). After territorial settlement, we reduced the availability of key breeding resources (i.e., nest boxes), generating heightened competition; within 24hr we reversed the manipulation, causing aggressive interactions to subside. We measured transcriptomic responses in the ovary during the peak of competition and 48hr after it ended, along with date-matched controls. Network analyses indicated that competing females experienced an immediate and temporary decrease in the expression of genes involved in the early stages of steroidogenesis; however, two days after competition had ended, there was a marked increase in the expression of genes involved in the final stages of sex steroid biosynthesis, including HSD17B1. In addition, ovaries that had been socially primed also displayed altered activity in gene networks related to the cell cycle, muscle performance, and extracellular matrix organization, which collectively point to social effects on future reproduction. Altogether, these findings show how the social environment shapes ovarian processes associated with both social behavior and adaptive transgenerational plasticity.

overall_design: ovaries were collected from 20 female tree swallows during peak competition (Day 0; n=6 experimental and n=5 controls) and two days after (Day 2; n=4 experimental and n=5 controls); total RNA was extracted and run on a Nextseq platform.

first: Alexandra

middle: B

last: Bentz

first: Tara

last: Empson

first: Elizabeth

middle: M

last: George

first: Douglas

last: Rusch

first: Aaron

last: Buechlein


title: Expression data from Arabidopsis autophagy mutants (atg5 and atg9) and wild type (Col-0)

status: Public on Oct 01 2021

city: Versailles

first: Celine

last: Masclaux-Daubresse

address: Route de Saint Cyr

country: France

institute: IJPB INRAE

summary:
Autophagy mutants display early yellowing phenotype and major metabolic changes under both ideal and limiting nitrate supplies.
We used Affymetrix microarrays to detail the global programme of gene expression underlying metabolic and cellular changes in autophagy mutants and wild type Arabidopsis rosettes grown under both low or high nitrate conditions. Fold changes data between mutants and wild type have been published (www.plantcell.org/cgi/doi/10.1105/tpc.114.124677)

overall_design: Three genotypes wild type (Col-0), atg5-3 mutant  (SALK_02060) and atg9 (SALK_130796) were grown under high nitrate (HN) for 30 days (T30) or low nitrate LN conditions for 30 days (T30) and 60 days (T60). Two consecutive cultures (C1 and C2) were performed at several month interval. For the two cultures and each genotype, rosettes of >6 plants were harvested  and mixed to extract RNA.

first: Kohki

last: Yoshimoto

first: Céline


title: Transcriptional profiling of the innate immune response in bovine cells

status: Public on Oct 02 2021

city: Boulder

first: Edward

last: Chuong

state: CO

address: 3415 Colorado Ave, JSC Biotech Bldg

department: BioFrontiers/MCDB

institute: University of Colorado Boulder

summary: Cattle are an important livestock species, and understanding the genomic architecture of agriculturally relevant traits such as disease susceptibility is of major interest in the bovine research community. Lineage-specific transposable elements (TEs) are a source of interferon-gamma (IFNG)-inducible regulatory elements that control human immune genes, but this possibility has been largely unexplored in other species that harbor distinct transposon landscapes, including cattle. We conducted transcriptomic and epigenomic profiling of the IFNG response in bovine cells, and found that ruminant-specific TEs are a major source of IFNG-inducible enhancer elements that shape bovine innate immune responses. CRISPR knockout experiments established that key immune genes including bovine IFNAR2 and IL2RB are regulated by TEs in MDBKs. Together with previous work in human cells, our findings demonstrate that lineage-specific TEs have been independently co-opted to regulate IFNG-inducible gene expression in at least two mammalian lineages. Therefore, TE co-option may mediate parallel evolutionary rewiring of mammalian immune regulation.

overall_design: Transcriptional profiling (RNA-seq) of wildtype bovine cell lines (MDBK, BL3.1) and primary monocytes and leukocytes that were either untreated or stimulated with 100 ng/mL interferon gamma (IFNG) for 2h or 4h. RNA-seq is also provided from clonal MDBK lines that stably express enAsCas12a or enAsCas12a and a pair of gRNAs targetting MER41_BT elements upstream of the IFNAR2 and IL2RB genes. All libraries from BL3.1 were sequenced twice. Each run is represented by a separate SRR.

first: Conor

middle: J

last: Kelly

first: Stacy

last: Bierman

first: Carol

middle: G

last: Chitko-McKown


title: The transcriptomic profile of wild-type and Ubr1-deletion Beauveria bassiana cultured in germination medium

city: Fuzhou

first: Dingyi

last: Wang

state: None Selected

address: Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China

country: China

institute: Fujian Normal University

summary: We report the application of RNA sequencing with Next Generation Sequencing technology for high-throughput status of transcripts in wild-type and ubr1-deletion Beauveria bassiana cultured in germination media (GM).

overall_design: The transcriptomic status of wild-type (WT) and Ubr1-deletion (ΔUbr1) strains grown on GM media

first: Yani

last: Mou


title: Chromatin profiling of the innate immune response in bovine MDBK cells

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin profiling (ATAC-seq) of a bovine cell line (MDBK) that was either untreated or treated with 100 ng/mL interferon gamma for 4h.


title: Transcriptional response of human duodenal enteroid monolayers to norovirus infection

city: Houston

first: Noah

last: Shroyer

state: Texas

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

institute: Baylor College of Medicine

summary: The goal of this study was to evaluate the transcriptional response of 4 human duodenal enteroid lines on monolayers to norovirus infections (GII.4). Enteroids were plated as monolayers in Intesticult (Stem Cell Technologies) proliferation medium. After 1 day of cell growth as a monolayer, the proliferation medium was changed with differentiation medium for 5 days. Five-day-differentiated monolayers were washed and were either mock-infected or inoculated with human norovirus supplemented with 500 μM glycochenodeoxycholic acid (GCDCA), for 1 to 2 h at 37°C.  Total RNA was extracted using the Qiagen RNeasy kit and paired-end Illumina sequencing was performed.

overall_design: A total of 8 mRNA profiles were generated by paired-end sequencing. The duodenal enteroid lines used were D4, D8, D104, and D109. Each of these cell lines were plated as monolayers on collagen, differentiated and mock-infected or inoculated with human norovirus supplemented with 500 μM GCDCA.

first: Sasirekha

last: Ramani

first: Mary

middle: K

last: Estes

first: Zachary

last: Criss

middle: F


title: CTRP3 exacerbates tendinopathy by dysregulating tendon stem cell differentiation and altering extracellular matrix composition

city: Seoul

first: Yongsik

last: Cho

address: 1 Gwanak-ro, Gwanak-gu, Seoul 08826. School of Biological Sciences, SNU

country: South Korea

institute: Seoul National Universiy

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptomic approaches in the brain at cell type resolution: Analysis of neuron-glia interaction in Plp1 and Cnp1 null-mutant mice

city: Munich

first: Moritz

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

country: Germany

summary: Global gene expression profiling is a powerful tool to obtain deep insights into  physiological and pathological cellular mechanisms. The enormous cellular complexity  of the mammalian brain, however, is a major obstacle for gene expression profiling.  Physiologically relevant changes of transcription that occur in specific cell populations  are likely to remain undetected in cellularly complex samples. The purification of single  populations of neural cell types eliminates these difficulties. We have approached this  problem in transgenic mice by labelling genetically-defined neural cell types that  express variants of GFP. When combined with isolation techniques such as  fluorescence activated cell sorting (FACS) or laser capture microdissection (LCM), the  isolation of intact RNA from unfixed cells for global transcriptome analysis is possible.  In this study we applied FACS and LCM to isolate neurons and glia to gain insight into  cell type specific gene expression. We profiled glial precursor cells, microglia and  oligodendrocytes using FACS and generated a transcriptome database for glial cell  types. LCM was used to study single isolated callosal projection neurons from the  cortex of mouse models, which develop adult onset axonal degeneration a hallmark of  many neurodegenerative diseases such as parkinson disease, Alzheimer disease and  Multiple Sclerosis (MS). The identification of molecular mechanisms underlying axonal  degeneration is critical to design rational therapies for neurodegenerative diseases.  Therefore we profiled wild type controls, Cnp1 and Plp1 null mutant mice (myelin  specific genes) at 4 different time points during adulthood. Cnp1 and Plp1 null mutants  show axonal swellings and with age severe neurodegeneration, although CNS myelin  seems ultra structural not affected.  In summary, we have shown the feasibility to snapshot gene expression profiles of  genetically defined neuronal subtypes in vivo and to compare morphologically similar  neurons at a given time in pathological conditions. We followed gene expression  changes starting from early disease states until stages of severe pathological signs,  focusing on cells known to be susceptible to a genetic predisposition. Our analysis  revealed several known and novel candidate genes and mechanisms that likely play a  role in the early adaptive responses of cortical projection neurons to cope with axonal  stress.

overall_design: For this study 1, 3, 6 and 12 month old male Cnp1-/-, Plp1-/Y and age-matched control mice (n = 3/genotype and timepoint) were used.

first: Sven

middle: P

last: Wichert


title: RNA-Sequencing analysis of adipose tissue from obese WT mice and AP2-Cre MCT1 knockout mice

city: Shanghai

first: Yijun

last: Lin

address: Yueyang Road

institute: Shanghai Institute of Nutrition and Health

summary: Adipose tissue is an active producer of lactate. In obesity, the increased size of adipocytes is accompanied by an increase in lactate production in adipose tissue, caused by hypoxia in obese adipocytes. How lactate affects metabolism in adipocyte and insulin sensitivity remains unclear. Here we develop a mouse model of MCT1,coding by Slc16a1, specific deletion in adipose tissues, using the AP2 promoter to drive Cre expression. This MCT1 AKO mice develop more severe insulin resistance in obesity with 16 weeks high fat diet treatment, while few changes happen to lipid metabolism in adipose tissues. We used RNA-seq to analyze the gene expression patterns of eWAT of obese MCT1 AKO mice compared to WT, and found significant changes in innate immune signaling and adipocyte apoptosis that reflect systemic inflammation and insulin resistance.

overall_design: We analyzed eWAT from 4 obese Slc16a1 flox/flox male mice (WT) and 4 obese AP2-cre Slc16a1 flox/flox male mice(AKO).

first: Yan

last: Chen


title: CTRP3 exacerbates tendinopathy by dysregulating tendon stem cell differentiation and altering extracellular matrix composition [seq]

summary: Tendinopathy, the most common disorder affecting tendons, is characterized by chronic disorganization of the tendon matrix, which eventually leads to tendon tear and rupture. The goal of this study was to identify a rational molecular target whose blockade can serve as a potential therapeutic intervention for tendinopathy. We identified C1q/TNF-related protein-3 (CTRP3) as a markedly upregulated cytokine in human and rodent tendinopathy. Overexpression of CTRP3 enhanced the progression of tendinopathy by accumulating cartilaginous proteoglycans and degenerating collagenous fibers in the mouse tendon, whereas CTRP3 knockdown suppressed the tendinopathy pathogenesis. Functional blockade of CTRP3 using a neutralizing antibody ameliorated overuse-induced tendinopathy of the Achilles and rotator cuff tendons. Mechanistically, CTRP3 elicited a transcriptomic pattern that stimulates abnormal differentiation of tendon stem/progenitor cells (TSPCs) and ectopic chondrification in tendons, as an effect linked to activation of Akt signaling. Collectively, we reveal an essential role for CTRP3 in tendinopathy and propose a potential therapeutic strategy for the treatment of tendinopathy.

overall_design: RNA sequencing data using samples from sham-operated and partially transected mouse Achilles tendons

first: Hyeon-Seop

last: Kim

first: Jin-Hong


title: Epigenomic profiling of the innate immune response in bovine MDBK cells

first: Edward

overall_design: Epigenomic (CUT&RUN) profiling of a bovine cell line (MDBK) that was either untreated or stimulated with 100 ng/mL interferon gamma (IFNG) for 2h. Libraries that were resequenced will have independent SRR, one for each sequencing run.


title: Arginine decarboxylase gene ADC2 regulates fiber elongation in cotton

first: Liangling

last: Shen

address: 389 Xincun Road

institute: Tongji Hospital, Tongji University

summary: ADC2 has a positive regulating effect on fiber elongation, which provides a basis for future cotton fiber development and research.

overall_design: Scanning electron microscopy showed that the fiber length was increased with exogenous addition of ADC product putrescine (Put) when compared with CK (water treatment). RNA-seq of Gossypium hirsutum treated with water (CK) or putrescine (put).

first: Hunjuan


title: PRMT5 promotes symmetric dimethylation of RNA processing proteins and modulates activated T cell alternative splicing and Ca2+/NFAT signaling

city: Columbus

first: Mireia

last: Guerau

state: OH

address: 460 Medical Center Drive, Rm 329

institute: The Ohio State University

summary: Protein Arginine Methyltransferase (PRMT) 5 is the major type 2 methyltransferase catalyzing symmetric dimethylation (SDM) of arginine. PRMT5 inhibition or deletion in CD4 Th cells reduces TcR engagement-induced IL-2 production and Th cell expansion and confers protection against experimental autoimmune encephalomyelitis (EAE), the animal model of Multiple Sclerosis. However, the mechanisms by which PRMT5 modulates T helper (Th) cell proliferation are still not completely understood and neither are the methylation targets in T cells. In this manuscript, we uncover the role of PRMT5 on alternative splicing (AS) in activated T cells and identify several targets of PRMT5 SDM involved in splicing. In addition, we find a possible link between PRMT5 mediated AS of Trpm4 (Transient Receptor Potential Cation Channel Subfamily M Member 4) and TcR/NFAT signaling/IL-2 production. This understanding may guide development of drugs targeting these processes to benefit patients with T cell-mediated diseases.

overall_design: Three biological replicates were analyzed for 2 conditions (Two genotypes and one treatment per genotype)

first: Shouvonik

last: Sengupta

first: Kelsi

middle: O

last: West

first: Shridhar

last: Sanghvi

first: Georgios

last: Laliotis

first: Laura

last: Agosto

first: Kristen

last: Lynch

first: Philip

last: Tsichlis

first: Harpreet

last: Singh

first: Kristin

last: Patrick


title: Genome-wide maps of Ets21C and Pointed isoforms PntP1 and PntP2 binding sites in intestinal stem cells (ISCs) and transcriptome profiling of ISCs over-expressing Spitz, Ets21C, PntP1, or PntP2

city: Salt Lake City

first: Bruce

middle: Alexander

last: Edgar

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary:
Purpose: The ETS transcription factors Ets21C and Pnt are downstream effectors of EGFR signaling pathway regulating intestinal stem cell (ISC) proliferation. ISC-specific DNA binding mapping using DamID and mRNA expression profiling were performed to identify the role of Ets21C and Pnt downstream of EGFR signaling.
Methods: For DamID, ISC were FACS sorted and their genomic DNA extracted, amplified, and sequenced. For RNA-Seq, ISC were FACS sorted and their total RNA extracted, amplified (only for Pnt samples), and sequenced.
Conclusions: We found that Ets21C and Pnt have a role in driving both ISC proliferation and metabolic changes.

overall_design: 4 biological replicates were performed for Ets21C DamID-Seq, 5 biological replicates for PntP1 and PntP2 DamID-Seq, 3 biological replicates for PntP1 RNA-Seq, 2 biological replicates for PntP2 RNA-Seq, and 3 biological replicates for Ets21C and Spitz RNA-Seq.

first: Zhang

last: Chenge

first: Yinhua

last: Jin

first: Marco

last: Marchetti


title: Temporal response of Mycobacterium tuberculosis H37Rv to vitamin C exposure in THP-1 macrophages.

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Transcriptional profiling of Mtb H37Rv infected into THP-1 macrophage cell line and treated with 100 µM vitamin C (vit C) for 96 hours and 144 hours, compared to gene expression profile of untreated bacteria post-infection.

overall_design: Agilent Mycobacterium tuberculosis 8x15 Microarray: AMADID: 026323

first: Kriti

last: Sikri

first: Kiran

last: Kumari

first: Jaya

middle: S

last: Tyagi


title: Single cell samples from Recessive Dystrophic Epidermolysis Bullosa (RDEB) patients before and after allogeneic epidermal grafting treatment

city: Minneapoilis

first: Julia

middle: Anne

last: Riedl

state: MN

address: 1600 Madison ST NE

department: Pediatrics

institute: University of Minnesota

summary: Single cell sequencing of RDEB samples after epidermal allogeneic grafting.

overall_design: Patient samples were take before and after epidermal grafting. There is also two WT control tissue samples from an epidermal graft plug and full-thickness skin.

first: Christen

last: Ebens

first: Jakub

last: Tolar


title: RNaseH2B single and compound mutant cerebellum

city: Memphis

first: Peter

last: McKinnon

state: Tennessee

address: 262 Danny Thomas Place

department: Center for Pediatric Neurological Disease Research

institute: St. Jude Children's Research Hospital

summary: We utilized RNA-seq analysis to examine the loss of RNaseH2B in the mouse cerebellum over time. We have looked at single and compound mutant knockouts at ages from postnatal day five, postnatal day twenty-eight and nine-week-old animals.

overall_design: RnaseH2B mutant RNA-seq total stranded from 9 week and p5, poly-A enriched for age p28.

first: Aditi

last: Aditi

first: Susanna

last: Downing

first: Patrick

last: Schreiner


title: Revealing regulatory transcription factors of aging in the kidney and kidney through multi-omics analysis

city: Boston

first: Yi

last: Zhang

state: MA

address: 200 Longwood Ave

department: PCMM

institute: Boston Children's Hospital

summary: Aging is accompanied by a gradual loss of systemic metabolic homeostasis, which is maintained by multiple-organs, especially the kidney and kidney. However, a systematic study of the regulatory networks and regulatory transcription factors (TFs) of aging in the kidney and kidney remains lacking. Here, we performed an integrated analysis of multi-omics datasets in the kidney and kidney from young and aged mice, including RNA-seq, reduced representation bisulfite sequencing (RRBS) and ATAC-seq datasets, which indicated that enhanced inflammation and dysregulated metabolism were conserved signatures in aged kidney and kidney in both the transcriptome and epigenome. Transcription factor and regulatory network analysis indicated that activation of AP-1 and SPI1 was responsible for enhanced inflammation, and down-regulation of HNFs and PPARs contributed to dysregulated metabolism in aged kidney and kidney. Importantly, we found that the activation of AP-1 was cellular autonomous in aged hepatic and renal cells. However, enhanced SPI1 was caused by elevated infiltration of macrophages. Importantly, inhibition of AP-1 with small molecule combination attenuated inflammation phenotypes of aging in vivo and in vitro. Taken together, our analysis revealed common signatures and regulatory TFs of aging in the kidney and kidney, providing novel targets for the development of anti-aging interventions.

overall_design: mRNA and ATAC-seq profiles of young and old kidney and kidney.

first: Yuting

last: Wang

first: Xiaojie

last: Yu

first: Yifan

last: Song


title: Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle [scRNA-seq]

city: South San Francisco

first: Bence

last: Daniel

state: CA

address: 1 DNA Way

department: Department Proteomic and Genomic Technologies

institute: Genentech Inc.

summary: Cell cycle (CC) is a fundamental biological process with robust, cyclical gene expression programs to facilitate cell division. In the immune system, a productive immune response requires the expansion of pathogen-responsive cell types, but whether CC also confers unique gene expression programs that inform the subsequent immunological response remains unclear. Here we demonstrate that single macrophages adopt different plasticity states in CC which is a major source of heterogeneity in response to polarizing cytokines. Specifically, macrophage plasticity to interferon gamma (IFNG) is substantially reduced, while interleukin 4 (IL-4) can induce S-G2/M-biased gene expression. Additionally, IL-4 polarization shifts the CC-phase distribution of the population towards G2/M phase, providing a mechanism for reduced IFNG-induced repolarization. Finally, we show that macrophages express tissue remodeling genes in the S-G2/M-phases of CC, that can be also detected in vivo during muscle regeneration. Therefore, CC defines macrophage inflammatory and regenerative responses in a cyclical, CC-phase-dependent manner.

overall_design: Examination of macrophage responses to polarizing cytokines with single cell RNA-seq.

last: Belk

first: Stefanie

last: Meier


title: HOST MICROBIOTA REGULATE SELECTIVE MYELOID SUBSETS IN THE CENTRAL NERVOUS SYSTEM DURING HOMEOSTASIS AND DISEASE

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University of Freiburg Medical Center

summary: The immune cells of the central nervous system (CNS) comprise parenchymal microglia and at the CNS border regions meningeal, perivascular and choroid plexus macrophages (summarized as CNS-associated macrophages, CAMs). Previous work has uncovered that microglial properties are strongly dependent on environmental signals from the commensal microbiota while its effect on CAMs remained unknown. By combining several microbiota manipulation approaches, genetic mouse models and single-cell RNA-sequencing, we comprehensively characterized CNS myeloid cell composition and function. Under steady-state, the transcriptional profile and numbers of choroid plexus macrophages were found to be tightly steered by complex microbiota. Divergently, perivascular and meningeal macrophages were affected to a lesser extent. An acute perturbation through viral infection evoked an attenuated immune response of all CAMs in germ-free mice. Additionally, we assessed CAMs in a more chronic pathological state in 5xFAD mice as a model for Alzheimer’s disease whereby exclusively perivascular macrophages displayed enhanced amyloid beta uptake in GF 5xFAD mice. Our results provide novel insights for understanding distinct microbiota-CNS macrophage interactions during health and perturbation that could potentially be targeted therapeutically.

overall_design: CNS-associated macrophages (CAMs) from the parenchyma, leptomeninges and choroid plexus were compared between mice housed in germ-free and controls housed in specific pathogen free conditions. Tissues from n ≥ 5 mice per group were pooled for higher cell yields of CAMs. The different CNS compartments were separated, and myeloid cells were isolated as previously described with minor modifications (Erny et al., 2015, Jordao et al., 2019).

first: Danel

last: Erny


title: Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle.


title: Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle [scATAC-seq]

overall_design: Examination of macrophage responses to polarizing cytokines with single cell ATAC-seq.


title: Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle [ChIP-seq]

overall_design: Examination of RNAPII binding during macrophage responses to polarizing cytokines.


title: Soluble adenylyl cyclase induces type 17 inflammation and is a potential therapeutic target in psoriasis

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

summary: Cyclic AMP (cAMP) has a key role in psoriasis pathogenesis, as indicated by the therapeutic efficacy of phosphodiesterase inhibitors that prevent the degradation of cAMP. However, whether soluble adenylate cyclase (sAC) (encoded by the ADCY10 gene), which is an important source for cAMP, is involved in Th17 cell-mediated inflammation or could be an alternative therapeutic target in psoriasis is unknown. We have utilized the imiquimod model of murine psoriasiform dermatitis to address this question. Adcy10-/- mice had reduced erythema, scaling and swelling in the skin and Th17 cell numbers in the draining lymph nodes, compared with wild-type mice after induction of psoriasiform dermatitis with imiquimod. During Th17 polarization in vitro, naïve T cells from Adcy10-/- mice were unable to differentiate to Th17 cells and RNA-seq analysis revealed that sAC was also essential for Th17 cell activation. Interestingly, sAC did not impact Th17 lineage-defining transcription factors (such as RORc and cMAF) but rather was required for CREB-dependent gene expression. Finally, topical application of small molecule sAC inhibitors (sACi) reduced imiquimod-induced psoriasiform dermatitis and IL17 gene expression in the skin. Collectively, these findings demonstrate that sAC is a key factor for inducing type 17 inflammation in the skin and sACi could provide an alternative class of topical therapeutics for psoriasis.

overall_design: Wild Type vs Adcy10-/- T cells following differentiation to Th17 cells in vitro, without or with polarizing cytokines

first: Jonathan

last: Zippin

first: Michael

middle: D

last: Reilly

first: Mahmoud

last: Eljalby

first: Rohan

last: Bareja


title: Neutrophil-specific defensin receptors prevent skin dysbiosis and bacterial infection

city: Baltimore

first: Xintong

last: Dong

state: MD

address: 725 N Wolfe St

department: Neuroscience

institute: Johns Hopkins University

summary: Healthy skin maintains a diverse microbiome and a potent immune system to fight off infections. In this study, we discovered that epithelium-derived antimicrobial peptides defensins activate orphan GPCRs Mrgpra2a/b on neutrophils.  This signaling axis is required for effective neutrophil-mediated skin immunity and microbiome homeostasis. We generated two mutant mouse lines, Defensin conditional knockout (Def cKO, K14-cre; Def fl/fl) in which the entire Def gene cluster is conditionally deleted from keratinocytes, and Mrgpra2 double knockout (Mrgpra2 dKO). We used high-throughput RNA sequencing to evaluate the whole transcriptomes of WT and mutant animals' skin under naive condition and 24 hours post-S. aureus infection. Disruption of defensin-Mrgpra2 signaling caused reduction of a network of pro-inflammatory and antibacterial gene expression. This study demonstrates the importance of epithelial-neutrophil signaling via the defensin-Mrgpra2 axis in maintaining healthy skin ecology and promoting antibacterial host defense.

overall_design: A total of 36 samples' Total RNA were purified from naïve or S. aureus infected skin of WT, Def cKO, and Mrgpra2 genoype dKO mice, with 6 biological replicates each.

first: Xinzhong


title: Adaptive local false discovery rate procedures for highly spiky data and their application to RNA sequencing data of yeast SET4 deletion mutants

first: Erin

last: Green

address: 1000 Hilltop Cir, Bs 325

department: Biological Sciences

institute: UMBC

summary: Genome-wide gene expression data were genertated for wildtype and set4 mutant yeast to determine the contribution of Set4 to gene expression under standard growth conditions. Illumina-based sequencing was performed on strand-specific libraries prepared from mRNA purified from yeast under standard (YPD-rich medium, no stress) growth conditions. Reads were procesed for qualiy control, mapped to the genome, and differential gene expression was determined using based on log fold-change difference between set4 mutants and wildtype. The distribution of the data was highly spiky and an adaptive local false discovery rate analysis was applied to analyze these data.

overall_design: Three replicates each of wildtype and set4 mutant yeast under normal growth conditions (YPD medium, 30 degrees C, no stress) are reported

first: Mark

last: Ramos

first: DoHwan

last: Park

first: Johan

last: Lim

first: Junyong

first: Khoa

last: Tran

first: Eric

last: Garcia


title: RNA-seq profiling of adult and late third instar larval testes from Drosophila melanogaster males and translocationsT(1;2) males

city: Bethesda

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: In order to study the effect of translocation T(1;2) on gene expression in testes, we performed polyA+ RNA-seq profiles from pools of adult and third instar larval testes from 7 translocation lines in biological quadruplicate. Among the 7 translocations, 5 are male sterile, 2 are fertile. In order to compare the expression profiles of translocations to the control, we sequence the testes from the parental flies that were irradiated to generate the translocation lines. We prepared 50bp stranded single end read libraries.

overall_design: We collected the dissected late third instar larval (L3) testes and one-to-five-day adult fly testes. We pooled 15 L3 testes and 20 adult testes for each sample (see "Extraction protocol" for details). Even though all the samples were collected on different days and stored at -80ºC until the RNA extraction, we extracted RNA and prepared the library simultaneously for all the samples in a 96 well plate.

first: Sharvani

last: Mahadevaraju


title: The Effects of Benoxacor on the Liver and Gut Microbiome of C57BL/6 Mice

city: Iowa City

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: We report the hepatotoxicity and effects of benoxacor on the gut microbiome following an acute oral exposure.

overall_design: Examination of RNA data to determine differentially expressed genes

first: Derek

middle: W

last: Simonsen

first: Hans-Joachim

last: Lehmler


title: YAP/TAZ-dependent transcriptome in cholangiocarcinoma cells

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: The Hippo pathway effectors yes-associated protein (YAP) and WW domain containing transcription regulator 1 (TAZ/WWTR1) support tumor initiation and progression in various cancer types. However, to which extent YAP and TAZ cooperatively contribute to cholangiocarcinoma (CCA) development and progression is poorly understood.   Our immunohistochemical studies showed that YAP and TAZ were expressed in different CCA subtypes. However, nuclear co-expression was not frequently detected. RNAinterference (RNAi) experiments illustrated that YAP and TAZ supported CCA cell viability. Comprehensive expression profiling of HUCCT-1 cells after combined silencing of YAP/TAZ revealed a potential impact on chromosomal instability.

overall_design: Gene-specific siRNAs (YAP1, YAP2, TAZ2, TAZ3) were transently transfected in HUCCT-1 cells. Nonsense/Scrambled siRNA-transfected and combined YAP/TAZ-specific siRNAs were used (in total 40 nM). Total mRNA was extracted 24 hours after transfection.

first: Kai

last: Breuhahn

first: Marcell

last: Tóth

last: De La Torre


title: Human Wilm' s tumor tissue: Case vs.Control

city: Beijing

first: Zhuo

last: Liu

address: Yabao Road 2

institute: Capital Institute of Pediatrics

summary: Genome-wide screeing of m6A-modified trancript in the Wilms’ tumor and adjacent normal tissue

overall_design: The immunoprecipitated RNA samples from adjacent non-cancerous tissue samples (n =3)and Wilms’ tumor groups (n = 5) were labeled with Cy5 fluorescent dye using Super RNA Labeling Kit (Arraystar) and purified using RNeasy Mini Kit. Cy5 labeled cRNAs were fragmented and hybridized to a mouse m6A epitranscriptomic microarray (8×60K, Arraystar) that contained 44,122 mRNA degenerate probes. The hybridized arrays were scanned using an Agilent Scanner G2505C.

first: Feng

last: He


title: Effect of SPARC on gene expression in HepG2

city: Suzhou

first: Shan

last: Wan

address: Renai Road 199

department: Pathology

institute: Soochow University

summary: This project focus on the effect of SPARC on liver cancer metastasis.

overall_design: HepG2 cells were treated with 200 ng/ml and 800 ng/ml recombinant SPARC. RNA and expression profiling was collected 24 hours after treatment.


title: MICU1 orchestrates the autophagic flux in a SPGL1- and VPS39-dependent manner

city: Bonn

first: Daniele

last: Bano

address: Sigmund-Freud-Strasse 27

institute: DZNE

summary: NOT PROVIDED; REQUESTED

overall_design: RNA-Seq of of wild-type, micu-1(bon20) and micu-1(bon20); mcu-1(ju1154) Caenorhaditis elegans

first: Joshua

last: Jackson

first: Lena

last: Wischhof

first: Enzo

last: Scifo

first: Anna

last: Pellizer

first: Yiru

last: Wang

first: Antonia

last: Piazzesi

first: Debora

last: Gentile

first: Sana

last: Siddig

first: Miriam

last: Stork

first: Chris

middle: E

last: Hopkins

first: Kristian

last: Händler

first: Andreas

last: Roos

first: Joachim

middle: L

last: Schultze

first: Pierluigi

last: Nicotera

first: Dan

last: Ehninger


title: Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle [RNA-seq]

first: Bence

last: Daniel

overall_design: Examination of macrophage responses to polarizing cytokines in the different pases of cell cycle.

first: Julia

last: Belk

first: Stefanie

last: Meier


title: Transcriptomic profiling of abiotic responses to drought, salt, ABA and SA in Phyllostachys edulis

city: Hangzhou

first: Haiwen

last: Lu

address: zhejiang A&F university, Lin 'an District, Hangzhou City, Zhejiang Province, China

institute: zhejiang A&F university

summary: Moso bamboo (Phyllostachys edulis (Carrière) J. Houz.), ) is one of the most importantessential economic bamboo species in China. However, the woods quality and yield of bamboo shoots were significantly threatened by diverse environmental conditions. significantly threaten the quality of wood and yield of bamboo shoots. In this study, to explore the molecular mechanism of abiotic stress response, we report the RNA-seq analyses of mosoMoso bamboo treated with drought, salt, SA and ABA at three -time courses. A total of 224.4 Gb clean data were generate in to explore the molecular mechanism of the abiotic stress response. The full-length transcriptome sequencing of these four treatments generated a total of 224.4 Gb data after quality trimming, and approximately 5.83Gban average of 6.615 Gb clean data were per sample was generated in per sample. The comparative analyses of the generated transcriptome data in this study will provide a valuable resource for identifying regulatory genes and potential pathways involved in various abiotic stresses in mosoMoso bamboo.

overall_design: RNA-seq analyses of moso bamboo treated with drought, salt, SA and ABA at three-time courses(0, 3, 24 h).

last: Hou

first: Naresh

last: Vasupalli

first: Xinchun

last: Lin


title: DNA methylation profiling identifies two distinct subgroups in breast cancers with low hormone receptor expression, mainly associated with HER2 amplification status

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

summary: Current clinical guidelines suggest that breast cancers with low hormone receptor expression (LowHR) in 1% to 10% of tumor cells should be regarded as hormone receptor positive tumors. However, clinical data shows that patients with such tumors have a worse outcome compared to patients with hormone receptor expression above 10 %. Further, gene expression studies suggest that these tumors have a TNBC-like signature similar to triple negative breast cancers (TNBC). The goal of this study was to use DNA methylation-based classification to clarify the status for this infrequent but important patient subgroup.   We performed whole genome DNA methylation profiling on 23 LowHR breast cancer specimens, including 13 samples with HER2 amplification and compared our results with a reference breast cancer cohort from The Cancer Genome Atlas.  Unsupervised clustering and dimensionality reduction revealed that breast cancers with low hormone receptor expression that lacked HER2 amplification usually clustered with TNBC reference samples (8/10; “LowHR TNBC-like”). In contrast, most specimens with low hormone receptor expression and HER2 amplification grouped with hormone receptor positive cancers (11/13; “LowHR HRpos-like”). We observed highly similar DNA methylation patterns of LowHR TNBC-like samples and true TNBCs with almost no differential methylation. Furthermore, the Ki67 proliferation index of LowHR TNBC-like samples as well as clinical outcome parameters were more similar to TNBCs and differed from LowHR_HRpos-like cases.   We here demonstrate that LowHR breast cancer comprises two molecularly distinct groups that can be separated by DNA methylation profiling. More clinical data is required for a definite classification of these tumors, but our data strongly suggests that LowHR TNBC-like samples are molecularly, histologically and clinically closely related to TNBC, while LowHR HRpos-like specimens are closely related to hormone receptor positive tumors.

overall_design: A total of 36 treatment-naive breast cancer biopsy specimens from the GeparSixto and GeparSepto trial were analyzed using the Illumina Infinium MethylationEPIC BeadChip, including 23 LowHR samples (ER/PR 1-10%) as well as 13 TNBC samples (ER/PR <1%)

first: David

last: Capper


title: RNAseq transcriptome analysis of Streptococcus pneumoniae 23F treated with PBT2 and zinc

city: Brisbane

middle: Manuel Pereira

last: De Oliveira

state: QLD

address: St Lucia

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

summary: Streptococcus pneumoniae is the primary cause of community-acquired bacterial pneumonia with rates of penicillin and multi-drug resistance exceeding 80% and 40%, respectively. The innate immune response uses various chemical insults to control infection, including metal stress mediated by localized changes in zinc abundance. Here, we characterized the impact of S. pneumoniae zinc intoxication revealing disruptions in central carbon metabolism, lipid biogenesis and peptidoglycan biosynthesis. To dysregulate zinc homeostasis in the wild-type strain, we investigated the safe-for-human use ionophore PBT2. PBT2 rendered wild-type S. pneumoniae strains sensitive to a range of antibiotics.

overall_design: For each species of S. pneumoniae 23F, 2 sample conditions in triplicate were analyzed. Sample conditions included: 1) bacterial treatment with cation-adjusted Muller Hinton broth (CA-MHB; reference sample); or 2)  CA-MHB + 32 µM PBT2 + 8 µM ZnSO4.

first: Lisa

last: Bolhmann

first: Mark

last: Walker

first: Christopher

last: McDevitt


title: Molecular mechanism of zero valent iron-enhanced microbial azo reduction in Shewanella decolorationis S12

city: Guangzhou

first: Yun

last: Fang

state: Guangzhou

address: 100 Central Xianlie Road

institute: Guangdong Institute of Microbiology

summary: Here, we established a successive Fe0-enhanced microbe system to remove azo dye (a typical organic pollutant) by Shewanella decolorationis S12 (S. decolorationis S12, an effective azo dye degradation bacterium) and examined the gene expression time course (10, 30, 60, and 120 min) in whole genome transcriptional level. Comparing with the treatment without ZVI, approximately 8% genes affiliated with 10 different gene expression profiles in S. decolorationis S12 were significantly changed in 120 min during the ZVI-enhanced microbial azo reduction. Intriguingly, MarR transcriptional factor might play a vital role in regulating ZVI-enhanced azo reduction in the aspect of energy production, iron homeostasis, and detoxification. Further investigation showed that induced [Ni-Fe] H2ase genes (hyaABCDEF) and azoreductase genes (mtrABC-omcA) contributed to ZVI-enhanced energy production, while reduced iron uptake (hmuVCB and feoAB), induced sulfate assimilation (cysPTWA) and cysteine biosynthesis (cysM) related genes were essential to iron homeostasis and detoxification. This study disentangles underlying mechanisms of ZVI-enhanced azo reduction in S. decolorationis S12 and lays a foundation for further optimization of integrated ZVI-microbial system for efficient organic pollution treatment.

overall_design: mRNA profiles of Shewanella decoloriationis S12 treated/untreated with Fe0 for 10, 30, 60, and 120 min were generated by deep sequencing, in triplicate, using Illumina Hiseq 2000.

first: Meiying

last: Xu


title: Epigenome analysis of autism spectrum disorder samples

city: Sao Paulo

first: Ana

middle: Carolina

last: Tahira

state: São Paulo

address: Avenida Vital Brasil, 1500 prédio 55

department: Parasitologia

country: Brazil

institute: Instituto Butantan

type: Methylation profiling by genome tiling array

summary: The aim of this study was to identify ASD vulnerability components, explore possible vulnerability subgroups, and evaluate environmental contribution to phenotypic variability.  We performed PCA and cluster analysis using ASD risk factor data. We found that PC1 had a higher correlation with psychosocial stress (maternal stress, maternal education, and social class), and PC2 a higher correlation with biological factors (Psychiatric Family History and Gestational Complications). Clustering analysis of PCA scores using bootstrap approach showed two clusters. Comparing the methylome between clusters we found 11.879 DMPs (p<0.05), and their CpG sites were enriched in VMRs, most showing environmental and genetic influences. Hypermethylated probes presented higher rates in  different regulatory regions associated with functional SNPs, indicating that the subgroups may have different affected regulatory regions and their liability to disease explained by common variations. Vulnerability score moderated by epigenetic clock was associated with Vineland Total score (p=0.0036, adjR2=0.31), suggesting risk factors with stress burden can influence phenotype.

overall_design: DNA from whole blood samples were treated using the EZ DNA Methylation kit (Zymo Research, Irvine, California,USA). The bisulfite converted DNA was hybridized in the BeadChip Human Methylation 450 microarrays (Illumina Inc., San Diego, California, USA) following the manufacturer’s protocol. Raw data was extracted by iScan SQ scanner using the GenomeStudio software (v.2011.1), with the methylation module v.1.9.0 IDAT files. Overall there 66 samples of ASD with diagnosed using ADI-R. IQ assessed by the SON-R 2½-7. Their functionality was assessed with Vineland, ASD severity with the CARS, and the patients’ internalizing and externalizing symptoms with the CBCL.

first: Vivi

middle: N

last: Reis

middle: C

first: Bianca

last: Lisboa

first: Vinicius

last: Gastaldi

last: Santos

first: Joana

last: Portolese

first: Helena

last: Brentani


title: Early-Stage Primary Anti-inflammatory Therapy Enhances Regenerative Efficacy of Platelet-Rich Plasma in a Rabbit Achilles Tendinopathy Model

first: Dengfeng

last: Ruan

state: China

address: 88 Jie Fang Road

department: Department of Orthopedic Surgery

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

summary: In this study, we aim to compare the therapeutic effects of PRP alone versus combination of PRP with primary glucocorticoid injection (GCI) at the early stage of tedinopathy. We hypothesize that PRP treatment could promote tendon regeneration through suppression of inflammation.

overall_design: We assigned the TSPCs into two experimental groups: TSPCs cultured in medium with or without 10% (v/v) PRP.

first: Chenqi

last: Tang

first: Yang

last: Fei

first: Shengjun

last: Qian

first: Xinyu

last: Xiang

first: Zizhan

last: Huang

first: Jialu

first: Xiao

last: Chen

first: Zi

last: Yin

first: Boon

last: Heng

first: Weishan

first: Wanlu

last: Liu

first: Weiliang

last: Shen

first: Hongwei

last: Ouyang


city: Chicago

first: Dolly

last: Mehta

state: Illinois

address: 835 S Wolcott Ave E403

department: Department of Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

summary: Analysis of transcriptional profile of lung resident macrophages during acute and resolution phase of LPS inhalation induced lung injury. Because macrophages coordinate both the induction and resolution of inflammatory lung injury, we examined the transcriptional signatures of resident lung macrophages isolated from LysM-GFP mice during baseline (0h), peak of injury (4h), and during the resolution phase (24h).

overall_design: Acute lung injury was induced in LysM-GFP mice through nebulization of a solution of LPS in saline (1mg/ml). At experimental timepoints, lungs were surgically removed, minced, and digested in a collogenase solution for 50min at 37 degrees, followed by mechanical separation by repeatedly passing tissue through a narrow gauge syringe. Single cell suspension was stained with florescently tagged antibodies for myeloid cell surface markers. Cells were isolated by FACS sorting: GFP+ cells were selected, followed by ly6g negative gating to exclude neutrophils, and CD64+ cells for mature macrophages. RNA from the sorted cells was collected in Trizol and isolated from cells via ethanol precipitation, then submitted for RNA sequencing.

first: Ian

last: Rochford


title: Different SP-1 binding dynamics at individual genomic loci

city: Boston

first: Yuko

last: Hasegawa

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

summary: Time-course ChIP-seq analysis of SP1-ERT2 that permits the measurement of SP1 binding dynamics at target sites on a genome-wide scale in human cells.

overall_design: Examination of genome-wide SP1-ERT2-3HA distribution at various time after tamoxifen induction in K562 cells. Spike-in control (yeast chromatin prepared from the strain expressing 3HA-TBP) was added to the sheared human chromatin lysate. We performed ChIP-seq of SP1-ERT2-3HA using single end sequencing. Reads were mapped to the custom genome containing human genome (hg38) and yeast genome (sacCer3).

first: Kevin

last: Struhl


title: Lignin production associated genes in Cenchrus purpueus

city: Juiz de Fora

first: Ana Luisa

middle: Sousa

last: Azevedo

state: Minas Gerais

address: Rua Eugenio do Nascimento, 610

institute: Empresa Brasileira de Pesquisa Agropecuaria

summary: This study aims to reveal genes related to lignin production in Cenchrus purpureus through RNA-Seq. This species is widely used as forrage for cattle, and for the last years, due to its high biomass yield, has been considered as source to lignocellulosic ethanol. Given those two importances, lignin is a molecule related to low digestibility in cattle and recalcitrance in biofuel production. Eight samples were chosen from previous lignin production  and forage quality data; four samples had low lignin production, and four had high lignin production. The highest nodes were collected for RNA extraction using TRIzol reagent, following Jordon-Thaden et a;. (2015) protocol. The cDNA library preparation was generated according to Illumina TruSeq Stranded mRNA Sample Prep kit protocol, and RNA sequencing was performed using HiSeq 2500 sequencer. Quality control was measured by FastQC software v 0.11.8. The sequenced reads were aligned to Cenchrus purpureus genome through STAR software v. 2.5.2b (Dobin et al., 2012). After that, the transcriptome was assembled using Stringtie v 2.0.4 software (Pertea et al., 2015). Salmon v 0.7.2 software (Patro et al., 2017) was used to quantify the sequenced reads. The DEG was identified using DESeq2 package, and genes functions were annotated through Trinotate software (Bryant et al., 2017). In total, approximately 130 million reads were sequenced. The final assembled transcriptome was formed by 101,169 transcripts. The differential expressed genes analysis revealed 52 significatively genes. Here, we highlighted genes related to sterol, L-serine and terpene biosynthetic process.

overall_design: We selected four low lignin production samples, and four high lignin production samples, according to previous study from the lab

first: Marco

middle: A

last: Machado


title: G-CSF SECRETED BY EPIGENETICALLY REPROGRAMMED MUTANT IDH1 GLIOMA STEM CELLS, REVERSES THE MYELOID CELLS'-MEDIATED IMMUNOSUPPRESSIVE TUMOR MICROENVIRONMENT

city: Ann Arbor

first: Maria

last: Castro

state: MI

address: 1150 West Medical Center Drive

department: Neurosurgery

institute: University of Michigan

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression profiling in epidydimal fat from wild-type and macrophage-derived TNF-α deficient mice.

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: The pro-inflammatory cytokine, tumor necrosis factor-alpha (TNF-α), has been suggested to be a key factor in the induction of obesity-associated metabolic dysfunction.  However, the role that macrophage-derived TNF-α has on regulating metabolic perturbations in obesity is not completely understood.  Therefore, we utilized the TNF-αFlox/FLox (F/F), LyzMcre+/- mouse model to determine the impact that macrophage TNF-α deletion has on the development of high-fat-diet (HFD)-induced obesity.

overall_design: 20 total samples were analyzed. We performed a pairwise comparison of macrophage-derived TNF-α deficient (cre) and wild-type (wt) genotypes. Genes with a p-valued < 0.05 and a fold-change ≥ 1.5 were selected.

first: Reilly

middle: T

last: Enos


title: The role of transcriptome and proteome in developmental competence of eggs of Sander lucioperca

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

summary: Molecular profiling of the eggs is an excellent approach aiming at understanding biological processes and mechanisms conditioning developmental competence in finfishes and, consequently, reproductive fitness. Despite many efforts, it is still unclear what is the specific role of transcriptome and proteome in determination of egg quality in Teleostei fishes. The aim of this study was to perform integrated transcriptomic-proteomic analysis of eggs of pikeperch – a commercially relevant freshwater fish species. Additionally, comparative analysis of transcriptome and proteome in eggs characterized by either high or low egg quality has been performed, in order to identify mechanisms leading to early embryonic lethality in pikeperch. Our study provides a novel insight into the understanding of the role of maternally-derived molecular cargo in finfishes. The data obtained sheds light on the importance of transcriptome in development of nervous system suggesting neurogenesis-related mRNAs as a very important, non-genetic inheritance factor. Proteomic analysis highlights specific role of proteins in the immune response in ovulated eggs. Integrated analysis brings attention to the galactose-specific lectin nattectin gene and protein as the frontline defense molecule for the egg and developing embryo. The molecular analysis of egg developmental competence emphasizes post-vitellogenic processes (final oocyte maturation and ovulation) as the ones potentially compromising transcriptomic profile, but not affecting proteomic cargo. It highlights the need for careful reconsideration of the commercial reproductive protocols as the very strong modulators of egg quality and their molecular profile. Considering the mechanisms driving these alterations as well as consequences stemming from the differential abundance of the transcripts are still to be explored, the candidate quality markers, first time provided for pikeperch along with the current study, are creating valuable resource for further studies.

overall_design: Comparative analysis of transcriptome in 10 eggs characterized by either high or low egg quality has been performed in pikeperch.

first: Daniel

last: Żarski

last: Le Cam

first: Thomas

last: Frohlich

first: Miwako

last: Kösters

first: Christophe

last: Klopp

first: Joanna

last: Nynca

first: Sławomir

last: Ciesielski

first: Beata

last: Sarosiek

first: Katarzyna

last: Dryl

first: Jerome

last: Montfort

first: Jarosław

last: Król

first: Pascal

last: Fontaine

first: Andrzej

last: Ciereszko

first: Julien

last: Bobe


title: Genome-wide analysis of m6A modification

city: Wuhan

first: Shan

last: Zhong

address: Donghu Road 185

institute: Wuhan University

summary: N6-methyladenosine (m6A) might exert stronger affection on circRNA expression, beyond linear genes.We confirmed the view by  analysing total RNA meRIP-Seq from GSE114150 and three other sets of data using RNA sequencing. Here, we study the difference in circRNA levels between wild (WT) and experimental (D395A-mutation; METTL3-knock-out) groups when m6A level changes. Results reveal knockout and D395A mutation of METTL3 could both increase the circRNA expression and the ratio of circular-to-linear. Our data propose a new pattern of circRNAs development and expand the understanding of m6A functions.

overall_design: mettl3 is knockedout using Crispr in embryonic stem cell in order to study the interaction between m(6)A and circRNA.

last: Xiao

first: Yujing

last: Han


title: GRIK2 is a target for bladder cancer stem-like cell-targeting immunotherapy

city: Sapporo

first: Yoshihiko

last: Hirohashi

address: South-1 West-17

country: Japan

institute: Sapporo Medical University

summary: Recent studies revealed that treatment resistant cancer stem-like cells (CSCs)/cancer-initiating cells (CICs) can be targeted by cytotoxic T lymphocytes (CTLs). CTLs recognize antigenic peptide derived from tumor-associated antigens (TAAs), thus identification of tumor-associated antigens (TAAs) expressed in CSCs/CICs is essential. Human leucocyte antigen (HLA) ligandome analysis using mass spectrometry enables analysis of naturally expressed antigenic peptides; however, HLA ligandome analysis requires large scale of sample and it is challenging for CSCs/CICs. In this study, we established novel bladder CSC/CIC model from a bladder cancer cell line UM-UC-3 cells using ALDEFLUOR assay. CSCs/CICs were isolated as aldehyde dehydrogenase (ALDH) high cells and several ALDHhigh clone cells were established. ALDHhigh clone cells were enriched with CSCs/CICs by sphere formation and tumorigenicity in immune deficient mouse. HLA ligandome analysis and gene expression (CAGE) using ALDHhigh clone cells revealed distinctive antigenic peptide repertoire in bladder CSCs/CICs, and we identified GRIK2 derived antigenic peptide is specifically expressed in CSCs/CICs. GRIK2 peptide-specific CTL clone recognized GRIK2-overexpressed UM-UC-3 cells and ALDHhigh clone cells indicating that GRIK2 peptide can be a novel target for bladder CSCs/CICs-targeting immunotherapy.

overall_design: Urothelial CSCs/CICs were isolated by an ALDEFLUOR assay fron human urothelial carcinoma cells, UM-UC-3. Aldehyde dehydrogenase-high (ALDHhigh) clone cell were isolated as urothelial CSCs/CICs. ALDHlow clone cells were isolated as urothelial non-CSCs/CICs. ALDHhigh clones (H-1, H-6, H-10) were used as CSCs/CICs clones and ALDHlow clones (L-1, L-3, L-8) were used as non-CSCs/CICs. Wild type UM-UC-3 cells were used as a control.

first: Haruka

last: Muyara


title: Role of microRNA-143, -150 and 126 in pathological retinal angiogenesis

city: Dublin

first: vikrant

last: singh

state: Ireland

address: 31 York Street

country: Ireland

institute: Royal college of Surgeons in Ireland

summary: Retinal neovascularization is a severe complication of proliferative diabetic retinopathy. We have previously identified that miRNAs is directly involved in the development of retinal neovascularization. Here, we explored the role of miRNAs and its underlying mechanism in modulating angiogenesis.

overall_design: Human dermal microvascular endothelial cells (HMEC-1) were transfected with synthetic human miRNA mimics (miR126, -143, and -150) and non-targeting scrambled RNAs.

first: Jiang

middle: H

last: Wang

first: Vikrant

last: Singh

first: Alex

last: Hewitt

first: Guei

last: Liu


title: Mapping the global chromatin connectivity network in colorectal cancer cell HCT116 and Oxaliplatin-resistant cell HCT116OxR [ATAC-seq]

city: Ji'nan

first: lian

middle: qing

last: jiao

state: Shandong Province

address: 247 Beiyuan Road

institute: the Second Hospital of Shandong University

summary: Numerous studies have highlighted the critical role of genetic and epigenetic modifications in the regulation of oxaliplatin resistance, but whether changes involving chromatin structure have not been fully investigated. We have integrated a variety of techniques to explore a comprehensive overview of chromatin changes in oxaliplatin-resistant processes.

overall_design: HCT116 cells and oxaliplatin-resistant HCT116 cells, HCT116OxR

first: Yunshan

first: Qinlian

last: Jiao


title: G-CSF SECRETED BY EPIGENETICALLY REPROGRAMMED MUTANT IDH1 GLIOMA STEM CELLS, REVERSES THE MYELOID CELLS'-MEDIATED IMMUNOSUPPRESSIVE TUMOR MICROENVIRONMENT [Run2961]

first: Maria

last: Castro

summary: Study the impact of IDH1 mutation in glioma on the tumor infiltrating myeloid cells phenotype and function

overall_design: Dissecting tumor heterogeneity in genetically engineered glioma mouse models expressing IDH1 mutation

first: Mahmoud

last: Alghamri

first: Ruthvik

last: Avvari


title: Mesenchymal (MES)- and Adrenergic (ADN) neuroblastoma cell line pair of isogenic origin

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: Cell line pair with different phenotypes were isolated from 1 patient to study intra-tumor heterogeneity in neuroblastoma

overall_design: Expression analysis of cell line pair with different phenotypes was used to study intra-tumor heterogeneity

first: Rogier

last: Versteeg

first: Mohamed

last: Hamdi

first: Ellen

last: Westerhout


title: Xenograft tumors of neuroblastoma cell lines

summary: Neuroblastoma cell lines SK-N-AS(-TRAIL) and SH-SY5Y were xenografted in mice to study them in vivo

overall_design: Expression analysis of a triplicate of xenograft tumors was used to study tumor growth in vivo compared to in vitro


title: Machine learning-assisted classification of responders and non-responders to bortezomib treatment regimens PAD and VCD using new experimental dataset of 58 multiple myeloma RNA sequencing profiles

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: Multiple myeloma (MM) is a hematological cancer which arises from abnormal antibody producing white blood plasma cells. MM affected approximately 500 000 people and results in ~100 000 deaths annually, being currently considered treatable but uncurable. There are several MM chemotherapy treatment regimens, among which ten include bortezomib, a proteasome-targeted drug. Patients with MM respond differently on bortezomib, and new prognostic biomarkers are needed to personalize treatments. However, there is a shortage of clinically annotated molecular profiles of MM that could be used to establish novel molecular diagnostics. In this study we report new molecular profiles for 58 MM patients annotated with data on two chemotherapy regimens which include bortezomib, doxorubicin, and dexamethasone (PAD) or bortezomib, cyclophosphamide, and dexamethasone (VCD). MM biosamples were taken prior to first line chemotherapy treatments and subjected to RNA sequencing.

first: Nicolas

last: Borisov

first: Anna

last: Sergeeva

last: Suntsova

first: Mikhail

last: Raevskiy


title: Effect of vitamin D treatment on myogenic differentiation of human umbilical cord tissue-derived mesenchymal stem cells

city: Faridabad

first: Suchitra

last: GOPINATH

address: NCR Biotech Science Cluster, 3rd Milestone,

institute: Translational Health Science and Technology Institute

summary: Transcriptomic analysis of vitamin D-treated human umbilical cord tissue-derived mesenchymal stem cells that were differentiated for 7 days into the myogenic lineage

overall_design: MSCs isolated from human umbilical cord tissue (UCT) and grown in αMEM with 20% fetal bovine serum on Laminin and Collagen Type 1-coated tissue culture plates were switched to medium containing αMEM with 15% KnockOut Serum Replacement. After 24 hours, MSCs from each of the biological replicates were treated with 100nM vitamin D or vehicle control for 3 days, with fresh medium being added every day. This was followed by induction of myogenic differentiation in both vitamin D-treated and untreated samples by the addition of medium containing 5% horse serum, 0.1 µM dexamethasone, and 50 µM hydrocortisone. After 7 days, total RNA was isolated from vitamin D-treated and control samples by Trizol (SIGMA) and processed for RNA-seq.

last: Gopinath


title: Expression data of micRNA from spleen CD4+CD25+ Treg cells

city: Shenyang

first: Hui

last: Feng

address: No.77 Puhe Road, Shenyang North New Area

institute: China Medical University

summary:
Treg plays a crucial immunomodulatory function. A few studies have confirmed the effects of parasite load on Treg cells phenotype and functions. We found that the plasmodium infection led to a particular micRNA profiles in Treg cells and influence the differentiation of Treg cells.
We used microarrays to detail the global programme of micRNA expression and identified distinct classes of up-regulated micRNA during this process.

overall_design: The mice spleen CD4+CD25+ Treg cells were sorted by MACS sorting for micRNA extraction and hybridization on Affymetrix micRNA arrays.We set two groups to analysis. Control group is normal BALB/c mice. Experimental group is BALB/c mice infected with P.y 17XL.

first: Yaming

last: Cao


title: Chromosome conformation capture by high thoughput sequencing (HiC) during Naïve CD4 T cell activation

city: Hong Kong SAR

first: Xiangzhi

last: Meng

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

summary: We report chromatin interaction changes before and early after naïve CD4 T cell activation.

overall_design: Human naïve CD4 T cells were isolated from periphery blood of 4 healthy donors. Cells were activated by CD3/CD28 beads for 0, 8 or 24 hours. 10 million cells were collected for HiC sequencing library preparation at each time point.


title: G-CSF SECRETED BY EPIGENETICALLY REPROGRAMMED MUTANT IDH1 GLIOMA STEM CELLS, REVERSES THE MYELOID CELLS'-MEDIATED IMMUNOSUPPRESSIVE TUMOR MICROENVIRONMENT [Run2943]

last: Castro

overall_design: Identification of the tumor-infiltrating myeloid cell's heterogeneity in genetically engineered glioma animal model expressing wild-type IDH or mutant IDH


title: G-CSF SECRETED BY EPIGENETICALLY REPROGRAMMED MUTANT IDH1 GLIOMA STEM CELLS, REVERSES THE MYELOID CELLS'-MEDIATED IMMUNOSUPPRESSIVE TUMOR MICROENVIRONMENT [Run1736]

summary: The purpose of this study was to characterize the molecular phenotype and function of tumor-infiltrating myeloid cells  isolated from genetically engineered glioma mouse model expressing wild-type IDH1 or mutated IDH1 (isocitrate dehydrogenase).

overall_design: Two groups of tumor infiltrating myeloid cells were isolated: mutant IDH tumor and wild type IDH tumor; three samples pre group.

last: Alghamri


title: Gene expression in bovine SCNT vs AI D30 foetal tissues (whole body with no head, no tail) in vivo developed in Holstein or Normande cows

city: Carrières sur Seine

first: Damien

last: VALOUR

state: Île-de-France

address: 34, rue Victor HUGO (Bât D)

summary: Evaluate the influence of somatic cell nuclear transfer on gene expression profiles in foetal tissues (whole bodies) at D30

overall_design: 4 replicates in SCNT, 4 replicates in AI (whole body) were hybridized (total N=8). Hybridization design: Dye Switch: N=8 slides were randomly hybridized using SCNT vs control (AI). SCNT foetal tissues (whole body) were once labelled with Cy3 against a first control (AI) and re-hybridized once labelled with Cy5 on another slide against the next control.

first: Isabelle

last: Hue

last: Valour

first: Anne

last: De la Foye

first: Ewa

last: Liszewska

first: Sophie

last: Pollet


title: G-CSF SECRETED BY EPIGENETICALLY REPROGRAMMED MUTANT IDH1 GLIOMA STEM CELLS, REVERSES THE MYELOID CELLS'-MEDIATED IMMUNOSUPPRESSIVE TUMOR MICROENVIRONMENT [human]

first: Maria

overall_design: Examining tumor-infiltrating immune cell identity in glioma patients with wild-type IDH1 or mutant IDH1 glioma

first: Mahmoud

first: Ruthvik

last: Avvari


title: RNA-Seq of LbDREB6 transgenic Populus ussuriensis

city: Harbin

first: Jingli

last: Yang

address: Hexing Road 51

institute: Northeast Forestry University

summary: For the RNA-seq experiments, 6-month old of  WT, OE14 and OE18 plants were grown under dewatered conditions (water withheld) for 1 weeks and harvested the fully expanded leaves.

overall_design: Samples were collected from three biological replicates.

first: Chenghao

last: Li

first: Hanzeng

last: Wang

first: Liu

last: Xiao


title: DNA methylation and RNA-seq data from mice liver of iron-disorder

status: Public on Sep 30 2021

city: Hangzhou

first: Li

last: Jiang

state: Zhejiang porvince

address: Number 866, Yuhangtang Road

institute: Zhejiang University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: We fed wild-type C57B/6J mice a standard-iron diet (SID) or either a high-iron diet (HID) or a low-iron diet (LID) to induce systemic iron overload or deficiency, respectively. Whole-genome bisulfate sequencing and RNA sequencing were then performed in the livers of SID-, HID-, and LID-fed mice.

overall_design: n=3 male mice each group

first: Zijun

last: Song

first: Junxia

last: Min

first: Fudi


title: Generation Sequencing Facilitates Quantitative Analysis of Wild Type and AGC1-4 Transcriptomes

city: Taian

first: yuying

last: zhang

address: No. 61 Mou Zong Street

institute: Shandong Agricultural University

summary: To further study the molecular mechanism of AGC1-4 in regulating the seed size and to search the genes that the transcription levels have been infected by AGC1-4 gene, we selected the siliques at the globular embryo stage at 3 days after pollination (DAP) from agc1-4 homozygous mutant and the wild-type separately and proceeded the RNA sequencing. Three biological replicates experiments were proceeded and six samples were obtained and a total of 137,259,154 reads were generated. A differentially expressed genes statistic was made under a standard of 1.5 fold change and P-value < 0.05. Compared with wild-type, 1611 differentially expressed genes (DEGs) were identified, including 996 up-regulated genes and 615 down-regulated genes.

overall_design: The siliques at 3 days after pollination (DAP)  from agc1-4 mutant and the wild-type were generated by the RNA sequencing, in triplicate, using the Illumina HiSeqTM 2500

first: Yu

middle: Y

last: Zhang


title: Similarities and differences in the acute-phase response to SARS-CoV-2 in rhesus macaques and African green monkeys

city: Covington

first: Joseph

last: Mudd

state: LA

address: 18703 Three Rivers rd

institute: Tulane University

summary: Understanding SARS-CoV-2 immune pathology is critical for the development of effective vaccines and treatments.  Here, we employed unbiased serial whole-blood transcriptome profiling by weighted gene network correlation analysis (WGCNA) at pre-specified timepoints of infection to understand SARS-CoV-2-related immune alterations in a cohort of rhesus macaques (RMs) and African green monkeys (AGMs) presenting with varying degrees of pulmonary pathology.  We found that the bulk of transcriptional changes occurred at day 3  post-infection and normalized to pre-infection levels by 3 weeks.  There was evidence of coordination of transcriptional networks in blood (defined by WGCNA) and the nasopharyngeal SARS-CoV-2 burden as well as the absolute monocyte count.  Pathway analysis of gene modules revealed prominent regulation of type I and type II interferon stimulated genes (ISGs) in both RMs and AGMs, with the latter species exhibiting a greater breadth of ISG upregulation.  Notably, pathways relating to neutrophil degranulation were enriched in blood of SARS-CoV-2 infected AGMs, but not RMs.  Our results elude to hallmark similarities as well as differences in the RM and AGM acute response to SARS-CoV-2 infection, and may help guide the selection of particular NHP species in modeling aspects of COVID-19 disease outcome.

sample_organism:
Macaca mulatta
Chlorocebus sabaeus

platform_organism:
Macaca mulatta
Chlorocebus sabaeus

overall_design: Examination of gene networks regulated in response to SARS-CoV-2 in rhesus macaques and African green monkeys


title: Neuroblastoma cell lines

first: Richard

last: Volckmann

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Neuroblastoma is composed of two super enhancer-associated differentiation states [ChIP-seq]

summary: Intra-tumour heterogeneity is increasingly appreciated as a determinant of tumour recurrence. Several tumour types were recently found to include phenotypically divergent cell types, reflecting lineage development stages (1,2,3). Lineage identity has been proposed to ensue super-enhancer (SE)-associated transcription factor (TF) networks (4,5), but their role in intra-tumour heterogeneity is unknown. Neuroblastoma is a paediatric tumour of the adrenergic differentiation lineage. Here we show that most neuroblastoma tumors include two types of tumor cells with highly diverging gene expression profiles. The undifferentiated mesenchymal cells and more differentiated adrenergic cells can interconvert and may relate to normal  lineage differentiation stages. ChIP-seq analysis of isogenic pairs of mesenchymal and adrenergic neuroblastoma cells revealed a distinct, highly consistent super-enhancer landscape for each cell type. Two SE-associated TF networks emerged that potentially master each cell type. Accordingly, the mesenchymal TF PRRX1 could reprogram the SE- and mRNA-profiles of adrenergic cells towards a mesenchymal state. To assess the clinical relevance of this bi-phasic system, we investigated chemo-sensitivity of both cell types. Mesenchymal cells were more resistant in vitro and were enriched in post-therapy and relapsed neuroblastoma in patients. Intra-tumor heterogeneity in neuroblastoma is therefore structured according to distinct SE-associated transcriptional programs that mediate a dynamic bi-phasic structure.

overall_design: Cultured cells were fixed with 1% formaldehyde. Nuclei were isolated and the DNA was sheared to 200 to 300 bp fragments. Histon-bound DNA was precipitated using antibodies H3K27Ac (#4729, Abcam).  De-crosslinked DNA was purified using Qiagen PCR purification kit (Qiagen) and quantified with Quant-IT Picogreen (Invitrogen). The DNA was used to generate sequencing libraries according to the manufactures procedure (Life Technologies): The DNA was end-polished, dA-tailed and adaptors with barcodes were ligated. The fragments were amplified (8 cycles) and quantified with a Bioanalyzer (Agilent). Libraries were prepped with the 5500W Flowchip v2 kit (Life Technologies)   libraries were sequenced using the HiSeq PE cluster kit v4 (Illumina) with the HiSeq 4000 platform (Illumina), resulting in 51-bp reads.

first: E

last: Westerhout

first: J

last: Koster

first: D

last: Zwijnenburg

first: R

last: Versteeg


title: The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma [scVDJ-seq]

city: Stanford

first: Aaron

middle: M

last: Newman

state: CA

address: 265 Campus Drive

department: Department of Biomedical Data Science

institute: Stanford University

summary: Biological heterogeneity in diffuse large B cell lymphoma (DLBCL) is partly driven by cell-of-origin subtypes and associated genomic lesions, but also by diverse cell types and cell states in the tumor microenvironment (TME). However, dissecting these cell states and their clinical relevance at scale remains challenging. Here, we implemented EcoTyper, a machine learning framework integrating transcriptome deconvolution and single-cell RNA sequencing, to characterize clinically relevant DLBCL cell states and ecosystems. Using this approach, we identified five cell states of malignant B cells that vary in prognostic associations and differentiation status. We also identified striking variation in cell states for 12 other lineages comprising the TME and forming cell-state interactions in stereotyped ecosystems. While cell-of-origin subtypes have distinct TME composition, DLBCL ecosystems capture clinical heterogeneity within existing subtypes and extend beyond cell-of-origin and genotypic classes. These results resolve the DLBCL microenvironment at unprecedented resolution and identify opportunities for therapeutic targeting (https://ecotyper-stanford-edu.stanford.idm.oclc.org/lymphoma).

overall_design:
Single cell B cell receptor sequencing of four DLBCL tumors (three ABC-DLBCL and one GCB-DLBCL).
>>> Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns. <<<

first: Chloé

middle: B

last: Steen

first: Bogdan

last: Luca

first: Ash

last: Alizadeh


title: Autophagy and lysosomal dysfunction in Tay Sachs disease are restored by mTOR modulation

city: Sevilla

first: Alejandro

last: Rubio

state: Sevilla

address: C/Utrera, Km1

department: Genética

country: Spain

institute: Universidad Pablo de Olavide

summary: Tay-Sachs disease (TSD) is a inherited lysosomal storage disease resulting from mutations in the α-subunits of the lysosomal enzyme, β-hexosaminidase A, and leads to excessive accumulation of GM2 ganglioside. This disease can be presented in infantil, juvenil and adult forms with rapid, progressive neurodegeneration. Although the link between mTOR and autophagy in Taysachs diseases has not been previously examined, it is reasonably to infer that reduced activity of HexA and the consequent intracellular accumulation of undegraded ganglyosides could lead accumulation of lysosomes, other substrates or dysfunctional organelles, similar to other defects detected in other LSD.  In the present study, we show that skin fibroblasts derived from PLS patients presented increased p62/SQSTM1 expression levels and autophagosome accumulation suggesting an impaired autophagic flux.

overall_design: We carry out a study of microarrays expression profiles in human samples under the following experimental conditions as well as possible alternative splicing events: healthy (HDFN), Sandhoff, Tay-sachs Infantile and Tay-sachs Juvenile

first: Beatriz

last: Castejón-Vega

first: Débora

last: Lendines-Cordero

first: Antonio

middle: J

last: Pérez-Pulido

first: Pedro

last: Bullón

first: José

last: Quiles

first: Jon

last: Lane

first: María

last: Cachón-González

first: Alberto

last: Sanz

first: Timothy

last: Cox

first: Elísabet

last: Alcocer-Gómez

first: Mario

last: Cordero


title: The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma


title: H3K27me3 and JMJD3 ChIP-seq during naïve CD4 T cell activation

first: Xiangzhi

last: Meng

summary: Histone modifications have been shown critically involved in transcriptional regulation, but the functions of histone modifiers and the impact of histone modifications in early transcription induction post CD4 T cell activation are unclear. We show here that JMJD3 binds to chromatin rapidly after naïve CD4 T cell activation, which is correlated with removal of H3K27me3 at promoter, enhancer and intronic regions.

overall_design: Human naïve CD4 T cells were isolated from periphery blood of healthy donors. Cells were activated by CD3/CD28 beads for 0, 8 or 24 hours. H3K27me3 and JMJD3 ChIP was performed.

first: Daniel

middle: R

last: Salomon


title: N6-adenomethylation of GsdmC is essential for Lgr5+ stem cell survival and normal colon epithelial morphogenesis

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago


title: Gene expression analysis on Naïve CD4 T cell with JMJD3 knockdown

summary: We report that knocking down JMJD3 in human naïve CD4 T cells impedes the induction of T cell activation related genes and cell cycle related genes.

overall_design: Human naïve CD4 T cells were isolated from periphery blood of healthy donors. Cells were transfected with siRNA knocking down JMJD3 (siJMJD3) or control siRNA (scrambled) by electroporation. 16 hours after electroporation, cells were activated by CD3/CD28 beads for 8 hours and collected for RNA purification.


title: N6-adenomethylation of GsdmC is essential for Lgr5+ stem cell survival and normal colon epithelial morphogenesis [scRNA-seq]

summary: The study explores the role of RNA methylation in the regulation of gut epithelial morphogenesis.

overall_design: Colonic crypt cells were isolated from 3 pairs of M14(flox/flox) and M14(flox/flox);Villin-Cre mice. The cells from each genotype were pooled and used for scRNA-seq.

first: Jie

last: Du

first: Lei

last: He

first: Weicheng

last: Liu

first: Wenjun

last: Kang

first: Wang

last: Liao

first: Tivoli

last: Nguyen

first: Zifeng

last: Deng

first: Urszula

last: Dougherty

first: Linda

last: Zhang

first: Rajesh

last: Sarkar

first: Sonia

middle: S

last: Kupfer

first: Mengjie

last: Chen

first: Joel

last: Pekow

first: Marc

last: Bissonnette

first: Chuan


title: Gene expression profiles of Caco-2 cells treated with cholic acid

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Colorectal cancer (CRC) is the third most common cancer in men and the second in women worldwide, with most of the case occurrences in developed regions. CRC can be induced by luminal factors, like dietary components and bile acids. Bile acids are metabolized from cholesterol in the liver, stored in the gallbladder and released into the small intestine upon meal ingestion to facilitate the absorption of dietary lipids and lipid-soluble vitamins. Bile acids are effectively reabsorbed at the distal ileum and returned to the liver, and only a small portion (~2-5%) enters the colon. Here primary bile acids, like cholic acid (CA) and chenodeoxycholic acid (CDCA) are deconjugated by bacteria and secondary bile acids are formed, such as deoxycholic acid (DCA), ursodeoxycholic acid (UDCA) and lithocholic acid. DCA is the major component of the colonic bile acid pool and is found to be increased upon a high fat diet. Moreover, high levels of DCA are known to increase the risk of colorectal cancer by inducing cytotoxicity to epithelial cells. In this study the cytotoxicity of Caco-2 cells to stimulation with cholic acid is investigated.

overall_design: Caco-2 cells were cultured on collagen-coated transwell or regular cell culture plates and incubated in the presence or absence of the bile acid cholate. Pooled RNA samples were subjected to expression profiling.

first: Anneke

last: Rijnierse

first: Noortje

last: IJssennagger

first: Michael

last: Müller

first: Roelof

last: van der Meer


title: Osimertinib resistant  cells of H1975

city: Xi'an

first: Kai

last: Li

address: NO.76, West Yanta Road

institute: Xi'an Jiaotong University

summary: To tentatively explored the latent roles of miRNAs in Osimertinib treatment response and tried to explore the methylation related miRNA maturation in the generation of resistance

overall_design: The established Osimertinib resistant adenocarcinoma cells of H1975OR were analyzed for gene-type signatures

first: Xin

last: Sun


title: Host Genes Differentially Expressed by Virulent and Attenuated Strains of Japanese Encephalitis Virus

city: Taipei

first: Jian-Jong

last: Liang

state: Taiwan

address: No.128 Academia Road, Section 2

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary:
Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus and causes acute encephalitis with high mortality rate in humans. Despite the demonstration of difference in neuroinvasiveness between JEV strains, little is known about host gene response upon infection of virulent and attenuated JEV strains. To understand the pathogenesis mechanism of JEV infection, we performed a comparative genome-wide microarray analysis (Affymetrix, mouse genome 430 2.0 with 45101 probe sets) of genes expressed in the mice brains three days post intracerebrally inoculated with JEV strains of different neurovirulence. We found that the virulent strain of JEV (RP-9) tended to affect the host gene expression more profoundly than the attenuated one (RP-2ms), as 961 vs. 665 and 655 vs. 509 genes were at least two-fold upregulated and downregulated by RP-9 and RP-2ms, respectively. In order to understand the host defense response against JEV, we further analyzed the microarray data with special focus on immune response. The expression levels of selected genes were further verified by quantitative RT-PCR at 1-, 3- and 5-day post JEV infection. The differentially regulated genes reported here likely contribute to the neurovirulent phenotype by modulating the host immunity, viral replication and/or cytotoxicity.
Keywords: day3, virus (1 x 10^4 PFU), intracerebrally (ic) inoculated, brain total RNA

overall_design:
Mice: 4~5-week-old C57BL/6.
Virus: JEV RP-9 (1 x 10^4 PFU), JEV RP2-ms (1 x 10^4 PFU), PBS (as control), intracerebrally (ic) inoculated.
Time course: The mice were sacrificed on day-1, day-3, and day-5 post-inoculation, and RNA from brain tissues were harvested by TRIZOL Reagent (Invitrogen).
DNA chip: Affymetrix Mouse Genome 430 2.0.
Data analysis: GeneSpring 7.2 (Silicon Genetics).

first: Yi-Ling

last: Lin


title: In Vitro Reconstitution of the Whole Male Germ-Cell Development from Mouse Pluripotent Stem Cells

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine


title: In Vitro Reconstitution of the Whole Male Germ-Cell Development from Mouse Pluripotent Stem Cells [PBAT]

summary: Mammalian male germ-cell development consists of three distinct phases: primordial germ cell (PGC) development, male germ-cell specification for spermatogonium development, and ensuing spermatogenesis. Here, we show an in vitro reconstitution of whole male germ-cell development by pluripotent stem cells (PSCs). Mouse embryonic stem cells (mESCs) are induced into PGC-like cells (mPGCLCs), which are expanded for epigenetic reprogramming. In reconstituted testes under an optimized condition, such mPGCLCs differentiate into spermatogonium-like cells with proper developmental transitions, gene expression, and cell-cycle dynamics and are expanded robustly as germline stem cell-like cells (GSCLCs) with an appropriate androgenetic epigenome. Importantly, GSCLCs show vigorous spermatogenesis, not only upon transplantation into testes in vivo but also under an in vitro culture of testis transplants, and the resultant spermatids contribute to fertile offspring. By uniting faithful recapitulations of the three phases of male germ-cell development, our study creates a paradigm for the in vitro male gametogenesis by PSCs.

overall_design: Methylome analysis of mouse spermatogonia and germline stem cell-like cells.

first: Yukiko

last: Ishikura

first: Hiroshi

last: Ohta

first: Takuya

last: Sato

first: Yusuke

last: Murase

first: Yoji

last: Kojima

first: Chika

last: Yamashiro

first: Tomonori

last: Nakamura

last: Yamamoto

first: Takehiko

last: Ogawa

first: Mitinori

last: Saitou


title: Different expression profiles of lncRNA, mRNA and circRNA in peripheral blood (ceRNA) of normal newborns and children with BPD.

city: Nanjing

first: Yufei

last: Chen

state: Jiangsu Province

address: 300 Guang Zhou Road

department: Department of Pediatrics

institute: The First Afﬁliated Hospital of Nanjing Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Increasing evidence shows that circular RNAs (circRNAs) play a vital role in the development of various diseases. A recent sequencing analysis of peripheral blood of bronchopulmonary dysplasia (BPD) patients showed that circABCC4 expression was significantly up-regulated. However, the specific function and potential mechanism of circRNAs in BPD remain unclear.

overall_design: Two peripheral blood samples of a normal newborn and a premature infant with BPD were included. There are no duplicate samples, control samples and/or reference samples or pigment exchanges.

first: xiaoqing

last: chen

first: yufei


title: The histone acetyltransferase HBO1 (KAT7) promotes efficient tip cell sprouting during angiogenesis

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Blood vessel growth and remodelling are essential during embryonic development and disease pathogenesis. The diversity of endothelial cells (ECs) is transcriptionally evident and ECs undergo dynamic changes in gene expression during vessel growth and remodelling.Here, we investigated the role of the histone acetyltransferase HBO1 (KAT7), which is important for activating genes during development and histone H3 lysine 14 acetylation (H3K14ac). Loss of HBO1 and H3K14ac impaired developmental sprouting angiogenesis and reduced pathological EC overgrowth in the retinal endothelium. Single-cell RNA-sequencing of retinal ECs revealed an increased abundance of tip cells in Hbo1 deleted retinas, which lead to EC overcrowding in the retinal sprouting front and prevented efficient tip cell migration. We found that H3K14ac was highly abundant in the endothelial genome in both intra- and intergenic regions suggesting that the role of HBO1 is as a genome organiser that promotes efficient tip cell behaviour necessary for sprouting angiogenesis.

overall_design: H3K14ac ChIP-seq in human umbilical vein endothelial cells (HUVECs)

first: Zoe

last: Grant

first: Anne

middle: K

last: Voss

first: Leigh

last: Coultas


title: Lipotoxic Injury Differentially Regulates Brain Microvascular Gene Expression in Male Mice

city: Davis

first: Saivageethi

last: Nuthikattu

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

summary:
Hyperlipidemia is a risk factor for vascular disease and dementia, and chronic consumption of a Western Diet (WD) correlates with cognitive impairment. However, the molecular mechanisms are poorly understood. This pilot study used microarrays to investigate the nutrigenomic pathways by which the WD and hyperlipidemia generated in the low-density lipoprotein receptor deficient (LDL-R -/-) male mouse regulate gene expression in the brain hippocampus microvessels.
Lipotoxic injury resulted in complex and multilevel molecular regulation of the hippocampal microvasculature involving transcriptional and post transcriptional regulation and may provide a molecular understanding for hyperlipidemia-associated dementia risk.

overall_design: Five-week-old LDL-R-/- (LDLR KO) and C57BL/6J wild type (WT) male mice were fed a chow (control diet, CD) or western diet (WD) for 8 weeks. Differential gene expression, gene networks and pathways, transcription factors, and non-protein coding RNAs were evaluated by genome-wide microarray and bioinformatics analysis of laser captured hippocampal microvessels of pool of n=3 biological replicates per each of the four experimental groups: WT CD, WT WD, LDLR KO CD and LDLR KO WD.

first: Dragan

last: Milenkovic

first: John

last: Rutledge

first: Amparo

last: Villablanca


title: The Landscape of Tumor Cell States and Ecosystems in Diffuse Large B Cell Lymphoma [scRNA-seq]

first: Aaron

last: Newman

overall_design:
Single cell sequencing of 14 sample pairs of B cells and non-B cells from 7 DLBCL tumors (n = 4; three ABC-DLBCL and one GCB-DLBCL), FL tumors (n = 3), and a patient with tonsilitis (n = 1)
>>> Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns. <<<

first: Chloé

last: Steen

first: Bogdan

last: Luca

first: Ash

last: Alizadeh


title: BRD4 (Bromodomain-Containing Protein 4) Interacts with GATA4 (GATA Binding Protein 4) to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes

city: Philadelphia

first: Ricardo

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

summary: In diseased organs, stress-activated signaling cascades alter chromatin, triggering broad shifts in transcription and cell state that exacerbate pathology. Fibroblast activation is a common stress response that worsens lung, liver, kidney and heart disease, yet its mechanistic basis remains poorly understood. Pharmacologic inhibition of the BET family of transcriptional coactivators alleviates cardiac dysfunction and associated fibrosis, providing a tool to mechanistically interrogate maladaptive fibroblast states and modulate their plasticity as a potential therapeutic approach. Here, we leverage dynamic single cell transcriptomic and epigenomic interrogation of heart tissue with and without BET inhibition to reveal a reversible transcriptional switch underlying stress-induced fibroblast activation. Transcriptomes of resident cardiac fibroblasts demonstrated robust and rapid toggling between the quiescent fibroblast and activated myofibroblast state in a manner that directly correlated with BET inhibitor exposure and cardiac function. Correlation of single cell chromatin accessibility with cardiac function revealed a novel set of reversibly accessible DNA elements that correlated with disease severity. Among the most dynamic elements was an enhancer regulating the transcription factor MEOX1, which was specifically expressed in activated myofibroblasts, occupied putative regulatory elements of a broad fibrotic gene program, and was required for TGFβ-induced myofibroblast activation. CRISPR interference of the most dynamic cis-element within the enhancer, marked by nascent transcription, prevented TGFβ-induced activation of Meox1. These findings identify MEOX1 as a central regulator of stress-induced myofibroblast activation associated with cardiac dysfunction. The plasticity and specificity of the BET-dependent regulation of MEOX1 in endogenous tissue fibroblasts provides new trans- and cis- targets for treating fibrotic disease.

overall_design: 16 samples from adult mouse cardiomyocytes were used for bulk RNAseq. 6 samples from embryonic heart tissues (developmental stage E14) were used for bulkRNAseq. 4 samples from adult mouse cardiomyocytes were used for bulk ATACseq.

first: Arun

last: Padmanabhan

first: Michael

last: Alexanian

first: Rajan

last: Jain

first: Deepak

last: Srivastava


title: N6-adenomethylation of GsdmC is essential for Lgr5+ stem cell survival and normal colon epithelial morphogenesis [bulk RNA-seq]

first: Yan

last: Li

overall_design: RNAs were prepared from purified colonic crypt cells of 3 pairs of M14(flox/flox) and M14(flox/flox);Villin-Cre mice. Poly-(A+) RNAs were used for RNA-seq in triplicates.

first: Jie

last: Du

first: Lei

last: He

first: Weicheng

last: Liu

first: Wenjun

last: Kang

first: Wang

last: Liao

first: Tivoli

last: Nguyen

first: Zifeng

last: Deng

first: Urszula

last: Dougherty

first: Linda

last: Zhang

first: Rajesh

last: Sarkar

first: Sonia

last: Kupfer

first: Mengjie

last: Chen

first: Joel

last: Pekow

first: Marc

last: Bissonnette

first: Chuan